Statistical Characterization of Eleven Kinds of Helix Elements with Amino Acid Residues in the Middle of Triplets

摘要

Based on the definition of a helix region in terms of dihedral angles φ and ψ, 681 helices could be easily extracted from 125 kinds of analyzed proteins by using two-dimensional φ and ψ diagrams of their three-dimensional structures. The 8000 (20~3) possible kinds of amino acid residues in the middle of triplets consisting of consecutive residues were used for a precise analysis of helical segments in globular proteins. They correspond to the 8000 kinds of amino acid residues in a sequence of proteins. The 681 helices were built up from 8836 amino acid residues, which could be classified into 11 kinds of helix elements (a-k). Each of the amino acid residues in a sequence of helical segments could be allotted to one of 11 helix elements (a-k). Glycine residues in the proteins were used for its precise assignment as internal standards. The 11 kinds of helix elements could be statistically characterized with amino acid residues in the middle of triplets. Amino acid residues, observed as a specific helix element 3-times or more often in the total helical segments, were evaluated regarding their propensities for a specific helix element by using their inherent preference (IP)-values for the specific helix element, which had been defined in a previous paper. Amino acid residues found 13-times or more often in the data set are also listed to show their propensities for specific helix elements.